Probabilistic 3D surface reconstruction from sparse MRI information

Surface reconstruction from magnetic resonance (MR) imaging data is indispensable in medical image analysis and clinical research. A reliable and effective reconstruction tool should: be fast in prediction of accurate well localised and high resolution models, evaluate prediction uncertainty, work with as little input data as possible. Current deep learning state of the art (SOTA) 3D reconstruction methods, however, often only produce shapes of limited variability positioned in a canonical position or lack uncertainty evaluation. In this paper, we present a novel probabilistic deep learning approach for concurrent 3D surface reconstruction from sparse 2D MR image data and aleatoric uncertainty prediction. Our method is capable of reconstructing large surface meshes from three quasi-orthogonal MR imaging slices from limited training sets whilst modelling the location of each mesh vertex through a Gaussian distribution. Prior shape information is encoded using a built-in linear principal component analysis (PCA) model. Extensive experiments on cardiac MR data show that our probabilistic approach successfully assesses prediction uncertainty while at the same time qualitatively and quantitatively outperforms SOTA methods in shape prediction. Compared to SOTA, we are capable of properly localising and orientating the prediction via the use of a spatially aware neural network.Comment: MICCAI 202

Fully automated, quality-controlled cardiac analysis from CMR: Validation and large-scale application to characterize cardiac function

OBJECTIVES: This study sought to develop a fully automated framework for cardiac function analysis from cardiac magnetic resonance (CMR), including comprehensive quality control (QC) algorithms to detect erroneous output. BACKGROUND: Analysis of cine CMR imaging using deep learning (DL) algorithms could automate ventricular function assessment. However, variable image quality, variability in phenotypes of disease, and unavoidable weaknesses in training of DL algorithms currently prevent their use in clinical practice. METHODS: The framework consists of a pre-analysis DL image QC, followed by a DL algorithm for biventricular segmentation in long-axis and short-axis views, myocardial feature-tracking (FT), and a post-analysis QC to detect erroneous results. The study validated the framework in healthy subjects and cardiac patients by comparison against manual analysis (n = 100) and evaluation of the QC steps' ability to detect erroneous results (n = 700). Next, this method was used to obtain reference values for cardiac function metrics from the UK Biobank. RESULTS: Automated analysis correlated highly with manual analysis for left and right ventricular volumes (all r > 0.95), strain (circumferential r = 0.89, longitudinal r > 0.89), and filling and ejection rates (all r ≥ 0.93). There was no significant bias for cardiac volumes and filling and ejection rates, except for right ventricular end-systolic volume (bias +1.80 ml; p = 0.01). The bias for FT strain was <1.3%. The sensitivity of detection of erroneous output was 95% for volume-derived parameters and 93% for FT strain. Finally, reference values were automatically derived from 2,029 CMR exams in healthy subjects. CONCLUSIONS: The study demonstrates a DL-based framework for automated, quality-controlled characterization of cardiac function from cine CMR, without the need for direct clinician oversight

Fairness in Cardiac Magnetic Resonance Imaging: Assessing Sex and Racial Bias in Deep Learning-Based Segmentation.

Background: Artificial intelligence (AI) techniques have been proposed for automation of cine CMR segmentation for functional quantification. However, in other applications AI models have been shown to have potential for sex and/or racial bias. The objective of this paper is to perform the first analysis of sex/racial bias in AI-based cine CMR segmentation using a large-scale database. Methods: A state-of-the-art deep learning (DL) model was used for automatic segmentation of both ventricles and the myocardium from cine short-axis CMR. The dataset consisted of end-diastole and end-systole short-axis cine CMR images of 5,903 subjects from the UK Biobank database (61.5 ± 7.1 years, 52% male, 81% white). To assess sex and racial bias, we compared Dice scores and errors in measurements of biventricular volumes and function between patients grouped by race and sex. To investigate whether segmentation bias could be explained by potential confounders, a multivariate linear regression and ANCOVA were performed. Results: Results on the overall population showed an excellent agreement between the manual and automatic segmentations. We found statistically significant differences in Dice scores between races (white ∼94% vs. minority ethnic groups 86-89%) as well as in absolute/relative errors in volumetric and functional measures, showing that the AI model was biased against minority racial groups, even after correction for possible confounders. The results of a multivariate linear regression analysis showed that no covariate could explain the Dice score bias between racial groups. However, for the Mixed and Black race groups, sex showed a weak positive association with the Dice score. The results of an ANCOVA analysis showed that race was the main factor that can explain the overall difference in Dice scores between racial groups. Conclusion: We have shown that racial bias can exist in DL-based cine CMR segmentation models when training with a database that is sex-balanced but not race-balanced such as the UK Biobank

Left Ventricular Shape and Motion Reconstruction through a Healthy Model for Characterizing Remodeling after Infarction

International audienceWe introduce a framework for the statistical characterization of heart remodeling from both shape and dynamics of the left ventricle. Shape was characterized by thickness and radius maps, unfolded in a two-dimensional dense Bull's eye. Motion was represented as a mixture of affine transformations in an anatomical space of coordinates. Using this representation, a population can be projected (after defining spa-tiotemporal correspondences) to an atlas space built for a given reference population-here, healthy subjects using a classic PCA approach-yielding a joint model of healthy shape and motion statistics. The reconstruction error on shape and motion can then be exploited to quantify remodeling abnormalities. We demonstrate these concepts on 48 healthy subjects and 62 patients with infarct (29 with one year follow-up) imaged with 3D echocardiography, analyzing a total of 139 sequences

Uncertainty Quantification in CNN-Based Surface Prediction Using Shape Priors

Surface reconstruction is a vital tool in a wide range of areas of medical image analysis and clinical research. Despite the fact that many methods have proposed solutions to the reconstruction problem, most, due to their deterministic nature, do not directly address the issue of quantifying uncertainty associated with their predictions. We remedy this by proposing a novel probabilistic deep learning approach capable of simultaneous surface reconstruction and associated uncertainty prediction. The method incorporates prior shape information in the form of a principal component analysis (PCA) model. Experiments using the UK Biobank data show that our probabilistic approach outperforms an analogous deterministic PCA-based method in the task of 2D organ delineation and quantifies uncertainty by formulating distributions over predicted surface vertex positions.Comment: Accepted to ShapeMI MICCAI 2018: Workshop on Shape in Medical Imagin

Learning interactions between cardiac shape and deformation: application to pulmonary hypertension

International audienceCardiac shape and deformation are two relevant descriptors for the characterization of cardiovascular diseases. It is also known that strong interactions exist between them depending on the disease. In clinical routine, these high dimensional descriptors are reduced to scalar values (ventricular ejection fraction, volumes, global strains...), leading to a substantial loss of information. Methods exist to better integrate these high-dimensional data by reducing the dimension and mixing heterogeneous descriptors. Nevertheless, they usually do not consider the interactions between the descriptors. In this paper, we propose to apply dimensionality reduction on high dimensional cardiac shape and deformation descriptors and take into account their interactions. We investigated two unsupervised linear approaches, an individual analysis of each feature (Principal Component Analysis), and a joint analysis of both features (Partial Least Squares) and related their output to the main characteristics of the studied pathology. We experimented both methods on right ventricular meshes from a population of 254 cases tracked along the cycle (154 with pulmonary hypertension, 100 controls). Despite similarities in the output space obtained by the two methods, substantial differences are observed in the reconstructed shape and deformation patterns along the principal modes of variation, in particular in regions of interest for the studied disease